data_2Q58 # _model_server_result.job_id gYlxsn9HjKFOaxiU7PUQ8Q _model_server_result.datetime_utc '2024-11-22 09:04:05' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 2q58 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1}' # _entry.id 2Q58 # _exptl.entry_id 2Q58 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 272.09 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ZOLEDRONIC ACID' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 2Q58 _cell.length_a 101.776 _cell.length_b 101.776 _cell.length_c 75.275 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Q58 _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 J N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 F O12 ZOL . A ZOL 1 1_555 C MG MG . A MG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? metalc ? metalc2 F O17 ZOL . A ZOL 1 1_555 C MG MG . A MG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc3 F O12 ZOL . A ZOL 1 1_555 D MG MG . A MG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc4 F O16 ZOL . A ZOL 1 1_555 E MG MG . A MG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc5 F O11 ZOL . A ZOL 1 1_555 E MG MG . A MG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc6 C MG MG . A MG 3 1_555 D MG MG . A MG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.073 ? metalc ? metalc7 C MG MG . A MG 3 1_555 A OD2 ASP 115 A ASP 1115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc8 C MG MG . A MG 3 1_555 A OD2 ASP 119 A ASP 1119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc9 C MG MG . A MG 3 1_555 K O HOH . A HOH 8002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc10 D MG MG . A MG 4 1_555 A OD1 ASP 115 A ASP 1115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc11 D MG MG . A MG 4 1_555 A OD2 ASP 119 A ASP 1119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc12 D MG MG . A MG 4 1_555 A OD1 ASP 119 A ASP 1119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.13 ? metalc ? metalc13 D MG MG . A MG 4 1_555 K O HOH . A HOH 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc14 E MG MG . A MG 5 1_555 A OD1 ASN 254 A ASN 1254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc15 E MG MG . A MG 5 1_555 K O HOH . A HOH 8006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc16 E MG MG . A MG 5 1_555 K O HOH . A HOH 8007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc17 E MG MG . A MG 5 1_555 K O HOH . A HOH 8008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc18 J O17 ZOL . B ZOL 2 1_555 G MG MG . B MG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc19 J O12 ZOL . B ZOL 2 1_555 G MG MG . B MG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.802 ? metalc ? metalc20 J O12 ZOL . B ZOL 2 1_555 H MG MG . B MG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc21 J O11 ZOL . B ZOL 2 1_555 I MG MG . B MG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc22 J O16 ZOL . B ZOL 2 1_555 I MG MG . B MG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc23 G MG MG . B MG 6 1_555 B OD2 ASP 115 B ASP 2115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? metalc ? metalc24 G MG MG . B MG 6 1_555 B OD2 ASP 119 B ASP 2119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? metalc ? metalc25 G MG MG . B MG 6 1_555 L O HOH . B HOH 8003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc26 G MG MG . B MG 6 1_555 L O HOH . B HOH 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc27 H MG MG . B MG 7 1_555 B OD1 ASP 115 B ASP 2115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.143 ? metalc ? metalc28 H MG MG . B MG 7 1_555 B OD2 ASP 119 B ASP 2119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc29 H MG MG . B MG 7 1_555 B OD2 ASP 187 B ASP 2187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.943 ? metalc ? metalc30 H MG MG . B MG 7 1_555 L O HOH . B HOH 8005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc31 I MG MG . B MG 8 1_555 B OD1 ASN 254 B ASN 2254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc32 I MG MG . B MG 8 1_555 L O HOH . B HOH 8009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc33 I MG MG . B MG 8 1_555 L O HOH . B HOH 8010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc34 I MG MG . B MG 8 1_555 L O HOH . B HOH 8011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? # _chem_comp.formula 'C5 H10 N2 O7 P2' _chem_comp.formula_weight 272.09 _chem_comp.id ZOL _chem_comp.mon_nstd_flag . _chem_comp.name 'ZOLEDRONIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(1-HYDROXY-2-IMIDAZOL-1-YLETHYLIDENE)DIPHOSPHONIC ACID' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O17 P14 ZOL sing 376 n n O17 H17 ZOL sing 377 n n P14 O16 ZOL sing 378 n n P14 O15 ZOL doub 379 n n P14 C8 ZOL sing 380 n n O16 H1 ZOL sing 381 n n C8 P9 ZOL sing 382 n n C8 O13 ZOL sing 383 n n C8 C7 ZOL sing 384 n n P9 O10 ZOL sing 385 n n P9 O11 ZOL sing 386 n n P9 O12 ZOL doub 387 n n O10 H10 ZOL sing 388 n n O11 H11 ZOL sing 389 n n O13 H13 ZOL sing 390 n n C7 N15 ZOL sing 391 n n C7 H71 ZOL sing 392 n n C7 H72 ZOL sing 393 n n N15 C16 ZOL sing 394 n y N15 C19 ZOL sing 395 n y C16 N17 ZOL doub 396 n y C16 H16 ZOL sing 397 n n N17 C18 ZOL sing 398 n y C18 C19 ZOL doub 399 n y C18 H18 ZOL sing 400 n n C19 H19 ZOL sing 401 n n # _atom_sites.entry_id 2Q58 _atom_sites.fract_transf_matrix[1][1] 0.009825 _atom_sites.fract_transf_matrix[1][2] 0.005673 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011346 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.013285 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 MG A 1 3 3 MG MG . D 2 MG A 1 4 4 MG MG . E 2 MG A 1 5 5 MG MG . F 3 ZOL A 1 1 1 ZOL ZOL . G 2 MG B 1 6 6 MG MG . H 2 MG B 1 7 7 MG MG . I 2 MG B 1 8 8 MG MG . J 3 ZOL B 1 2 2 ZOL ZOL . K 4 HOH A 1 8001 8001 HOH HOH . K 4 HOH A 2 8002 8002 HOH HOH . K 4 HOH A 3 8006 8006 HOH HOH . K 4 HOH A 4 8007 8007 HOH HOH . K 4 HOH A 5 8008 8008 HOH HOH . K 4 HOH A 6 8014 8014 HOH HOH . K 4 HOH A 7 8017 8017 HOH HOH . K 4 HOH A 8 8018 8018 HOH HOH . K 4 HOH A 9 8020 8020 HOH HOH . K 4 HOH A 10 8021 8021 HOH HOH . K 4 HOH A 11 8022 8022 HOH HOH . K 4 HOH A 12 8024 8024 HOH HOH . K 4 HOH A 13 8026 8026 HOH HOH . K 4 HOH A 14 8029 8029 HOH HOH . L 4 HOH B 1 8003 8003 HOH HOH . L 4 HOH B 2 8004 8004 HOH HOH . L 4 HOH B 3 8005 8005 HOH HOH . L 4 HOH B 4 8009 8009 HOH HOH . L 4 HOH B 5 8010 8010 HOH HOH . L 4 HOH B 6 8011 8011 HOH HOH . L 4 HOH B 7 8012 8012 HOH HOH . L 4 HOH B 8 8013 8013 HOH HOH . L 4 HOH B 9 8015 8015 HOH HOH . L 4 HOH B 10 8016 8016 HOH HOH . L 4 HOH B 11 8019 8019 HOH HOH . L 4 HOH B 12 8023 8023 HOH HOH . L 4 HOH B 13 8025 8025 HOH HOH . L 4 HOH B 14 8027 8027 HOH HOH . L 4 HOH B 15 8028 8028 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 O O17 ZOL . . . F 3 -0.83 17.16 53.086 1 40.96 ? O17 ZOL 1 A 1 HETATM 2 P P14 ZOL . . . F 3 0.18 16.493 52.204 1 61.28 ? P14 ZOL 1 A 1 HETATM 3 O O16 ZOL . . . F 3 -0.52 15.812 50.933 1 86.71 ? O16 ZOL 1 A 1 HETATM 4 O O15 ZOL . . . F 3 1.074 15.376 52.9 1 50.17 ? O15 ZOL 1 A 1 HETATM 5 C C8 ZOL . . . F 3 1.391 17.708 51.572 1 61 ? C8 ZOL 1 A 1 HETATM 6 P P9 ZOL . . . F 3 0.519 19.045 50.688 1 58.31 ? P9 ZOL 1 A 1 HETATM 7 O O10 ZOL . . . F 3 1.703 20.028 50.222 1 70.29 ? O10 ZOL 1 A 1 HETATM 8 O O11 ZOL . . . F 3 -0.086 18.375 49.373 1 60.14 ? O11 ZOL 1 A 1 HETATM 9 O O12 ZOL . . . F 3 -0.472 19.755 51.546 1 44.88 ? O12 ZOL 1 A 1 HETATM 10 O O13 ZOL . . . F 3 2.278 17.046 50.652 1 50.37 ? O13 ZOL 1 A 1 HETATM 11 C C7 ZOL . . . F 3 2.23 18.305 52.76 1 57.97 ? C7 ZOL 1 A 1 HETATM 12 N N15 ZOL . . . F 3 3.372 19.151 52.409 1 51.54 ? N15 ZOL 1 A 1 HETATM 13 C C16 ZOL . . . F 3 4.311 18.865 51.556 1 56.52 ? C16 ZOL 1 A 1 HETATM 14 N N17 ZOL . . . F 3 5.133 19.809 51.506 1 54.95 ? N17 ZOL 1 A 1 HETATM 15 C C18 ZOL . . . F 3 4.74 20.859 52.406 1 49.31 ? C18 ZOL 1 A 1 HETATM 16 C C19 ZOL . . . F 3 3.595 20.357 52.907 1 48.89 ? C19 ZOL 1 A 1 # _model_server_stats.io_time_ms 99 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 16 #